[gmx-users] SEP and HO atom type

[Luciane Vieira de Mello]

Hi David,

thanks for your mail.
But, the problem is not in the SEP definition. If I run grompp using just
the protein everything goes fine. But, when the ligand is included, which
contains the HO atom, grompp says Atomtype 'HO' not found!
The ligand was included in the .top file after pdb2gmx for the protein,
since the ligand topology was made outside gromacs.
in the ligand.itp:

 [ atoms ]
 ;  nr  type resnr resid  atom  cgnr charge
     1    OM     1 GAD      O1     1   -0.635
     2     C     1 GAD      C1     1    0.270
     3    OM     1 GAD      O2     1   -0.635
     4   CH1     1 GAD      C2     2    0.150
     5    OA     1 GAD     O1P     2   -0.548
     6    HO     1 GAD     HAB     2    0.398
     7   CH2     1 GAD      C3     3    0.150
     8    OA     1 GAD      O3     3   -0.548
     9    HO     1 GAD     HAA     3    0.398


Any idea?

thanks in advance.




> Because the rtp defines an atom that is not in the itp files of the
> force field. However, HO is a normal alcohol hydrogen that should be in
> there. Check the definitions of SEP etc. in your rtp file and compare
> them to the itp file. Do also look in your top file to see whether atom
> names have been translated appropriately into atomtypes.
>
> > thanks in advance
> >
> > +-------------------------------------------------------------------------+
> > |                  Dra. Luciane Vieira de Mello Rigden                    |
> > | e-mail: mello at cenargen.embrapa.br                                       |
> > | Embrapa Recursos Geneticos e Biotecnologia                              |
> > | Parque Estacao Biologica           |  http://www.cenargen.embrapa.br    |
> > | PqEB - Final - Av. W3 Norte        |  Phone:  +55 (61)448-4741          |
> > | 70770-900, Brasilia-D.F.-BRAZIL    |  Fax:    +55 (61)340-3658          |
> > +-------------------------------------------------------------------------+
> >
> >
> >
> > On Tue, 4 Feb 2003, Anton Feenstra wrote:
> >
> > > Luciane Vieira de Mello wrote:
> > > [...]
> > > > I am not sure if I am checking the right file:
> > > > ffG43a1nb.itp
> > > > where I tried to add the HO atomtype from ffgmx2nb.itp, including the
> > > > pairtypes.
> > >
> > > There is also a .atp file (for Atom TyPes), but IIRC that is only
> > > used by pdb2gmx and not grompp... ;-(
> > >
> > >
> > > --
> > > Groetjes,
> > >
> > > Anton
> > >   ________ ___________________________________________________________
> > > |        | Anton Feenstra                                            |
> > > | .      | Dept. of Pharmacochemistry - Vrije Universiteit Amsterdam |
> > > | |----  | De Boelelaan 1083 - 1081 HV Amsterdam - The Netherlands   |
> > > | |----  | Tel: +31 20 44 47608 - Fax: +31 20 44 47610               |
> > > | ' __   | Feenstra at chem.vu.nl - http://www.chem.vu.nl/afdelingen/FAR|
> > > |  /  \  |-----------------------------------------------------------|
> > > | (    ) | Dept. of Biophysical Chemistry - University of Groningen  |
> > > |  \__/  | Nijenborgh 4 - 9747 AG Groningen - The Netherlands        |
> > > |   __   | Tel +31 50 363 4327 - Fax +31 50 363 4800                 |
> > > |  /  \  | K.A.Feenstra at chem.rug.nl - http://md.chem.rug.nl/~anton   |
> > > | (    ) |-----------------------------------------------------------|
> > > |  \__/  | "If You See Me Getting High, Knock Me Down"               |
> > > |        | (Red Hot Chili Peppers)                                   |
> > > |________|___________________________________________________________|
> > >
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> --
> Groeten, David.
> ________________________________________________________________________
> Dr. David van der Spoel, 	Dept. of Cell and Molecular Biology
> Husargatan 3, Box 596,  	75124 Uppsala, Sweden
> phone:	46 18 471 4205		fax: 46 18 511 755
> spoel at xray.bmc.uu.se	spoel at gromacs.org   http://xray.bmc.uu.se/~spoel
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